{'WT': '../test/Moazzen/WT_E11_5/sample_filtered_feature_bc_matrix', 'KO': '../test/Moazzen/Mut_E11_5/sample_filtered_feature_bc_matrix'}
{'WT': '../test/Moazzen/WT_E11_5/sample_filtered_feature_bc_matrix', 'KO': '../test/Moazzen/Mut_E11_5/sample_filtered_feature_bc_matrix'}
Quality PlotsΒΆ
Basic QC plots & metricsΒΆ
Table of basic QC metricsΒΆ
| n_genes_by_counts | total_counts | pct_counts_mt | pct_counts_ribo | doublet_score | S_score | G2M_score | sample | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| mean | median | mean | median | mean | median | mean | median | mean | median | mean | median | mean | median | size | |
| sample | |||||||||||||||
| KO | 3193.389 | 2561.0 | 14489.261 | 5980.0 | 3.160 | 1.877 | 0.0 | 0.0 | 0.049 | 0.037 | -0.005 | -0.149 | -0.005 | -0.149 | 8365 |
| WT | 3272.712 | 2674.0 | 15085.768 | 6799.0 | 2.417 | 1.591 | 0.0 | 0.0 | 0.045 | 0.029 | 0.003 | -0.148 | 0.003 | -0.148 | 11229 |
HistogramsΒΆ
Filtering ThresholdsΒΆ
| Min | Max | |
|---|---|---|
| n_genes_by_counts | 155.0 | 10186.347402 |
| total_counts | 1059.0 | 35071.109421 |
Number of outliers based on provided criteriaΒΆ
| Outlier | MT-Outlier | ||
|---|---|---|---|
| sample | |||
| False | WT | 8429 | 10040 |
| KO | 7051 | 7010 | |
| True | WT | 2800 | 1189 |
| KO | 1314 | 1355 |
Remaining Cells after filtering based on outlier functionΒΆ
| n_genes_by_counts | total_counts | pct_counts_mt | pct_counts_ribo | doublet_score | S_score | G2M_score | sample | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| mean | median | mean | median | mean | median | mean | median | mean | median | mean | median | mean | median | size | |
| sample | |||||||||||||||
| KO | 3418.461 | 2866.0 | 12968.836 | 5597.0 | 2.128 | 1.813 | 0.0 | 0.0 | 0.049 | 0.039 | -0.015 | -0.157 | -0.015 | -0.157 | 5739 |
| WT | 3792.106 | 3361.0 | 13962.100 | 6637.0 | 2.248 | 1.979 | 0.0 | 0.0 | 0.049 | 0.034 | 0.033 | -0.099 | 0.033 | -0.099 | 7248 |
Scatter plots of confoundersΒΆ
DecontX contaminationΒΆ
Clustering prior to cell filteringΒΆ
Regression of VariablesΒΆ
| sample | n_genes_by_counts | log1p_n_genes_by_counts | total_counts | log1p_total_counts | pct_counts_in_top_20_genes | total_counts_mt | log1p_total_counts_mt | pct_counts_mt | total_counts_ribo | ... | decontX_contamination | decontX_clusters | n_genes | doublet_score | predicted_doublet | n_counts | S_score | G2M_score | phase | groups | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AAACAAGCAATGAGCCAACGGGAA-1 | WT | 2957 | 7.992269 | 5382.0 | 8.591002 | 8.286882 | 76.0 | 4.343805 | 1.412115 | 0.0 | ... | 0.013997 | 1 | 2957 | 0.033079 | False | 5382.0 | 0.708197 | 0.708197 | S | 0 |
| AAACAAGCACAGCAACAACGGGAA-1 | WT | 843 | 6.738152 | 2423.0 | 7.793174 | 27.445316 | 10.0 | 2.397895 | 0.412712 | 0.0 | ... | 0.044109 | 3 | 843 | 0.023555 | False | 2423.0 | -0.412892 | -0.412892 | G1 | 1 |
| AAACAAGCAGAGGCTTAACGGGAA-1 | WT | 2261 | 7.724005 | 3429.0 | 8.140316 | 6.824147 | 32.0 | 3.496508 | 0.933217 | 0.0 | ... | 0.031528 | 1 | 2261 | 0.018878 | False | 3429.0 | -0.356001 | -0.356001 | G1 | 0 |
| AAACAAGCATCGATAGACTTTAGG-1 | WT | 5243 | 8.564840 | 12701.0 | 9.449514 | 3.999685 | 41.0 | 3.737670 | 0.322809 | 0.0 | ... | 0.026544 | 2 | 5243 | 0.014218 | False | 12701.0 | 0.733244 | 0.733244 | S | 3 |
| AAACAAGCATTGCCCAACTTTAGG-1 | WT | 3307 | 8.104099 | 6492.0 | 8.778480 | 10.921134 | 96.0 | 4.574711 | 1.478743 | 0.0 | ... | 0.037526 | 1 | 3307 | 0.043515 | False | 6492.0 | 0.123662 | 0.123662 | S | 0 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| TTTGTGAGTAGGTGACATGTTGAC-1 | KO | 5887 | 8.680672 | 16686.0 | 9.722385 | 7.473331 | 459.0 | 6.131227 | 2.750809 | 0.0 | ... | 0.069692 | 2 | 5887 | 0.235832 | False | 16686.0 | 0.195697 | 0.195697 | S | 4 |
| TTTGTGAGTCCACAATATGTTGAC-1 | KO | 6926 | 8.843182 | 26409.0 | 10.181498 | 6.232724 | 439.0 | 6.086775 | 1.662312 | 0.0 | ... | 0.051976 | 1 | 6925 | 0.041409 | False | 26409.0 | -0.138252 | -0.138252 | G1 | 8 |
| TTTGTGAGTGAACGGTATGTTGAC-1 | KO | 4322 | 8.371705 | 11396.0 | 9.341105 | 12.267462 | 275.0 | 5.620401 | 2.413127 | 0.0 | ... | 0.154473 | 1 | 4322 | 0.084693 | False | 11396.0 | -0.109296 | -0.109296 | G1 | 9 |
| TTTGTGAGTGCTGATTATGTTGAC-1 | KO | 3852 | 8.256607 | 8126.0 | 9.002947 | 8.983510 | 81.0 | 4.406719 | 0.996800 | 0.0 | ... | 0.402884 | 2 | 3852 | 0.169399 | False | 8126.0 | -0.218594 | -0.218594 | G1 | 7 |
| TTTGTGAGTTACCGTGAGTAGGCT-1 | KO | 1393 | 7.239933 | 2029.0 | 7.615791 | 8.378512 | 25.0 | 3.258096 | 1.232134 | 0.0 | ... | 0.155729 | 1 | 1393 | 0.037975 | False | 2029.0 | -0.329304 | -0.329304 | G1 | 2 |
12987 rows Γ 27 columns
Ambient RNAΒΆ
<Axes: xlabel='decontX_clusters', ylabel='decontX_contamination'>
Session InformationΒΆ
Click to view session information
----- anndata 0.10.7 matplotlib 3.8.4 numpy 1.26.4 pandas 2.2.2 patchworklib 0.6.3 requests 2.32.3 scanpy 1.10.1 scipy 1.13.1 seaborn 0.13.2 session_info 1.0.0 tomlkit 0.12.5 -----
Click to view modules imported as dependencies
PIL 10.3.0 anyio NA argcomplete NA arrow 1.3.0 asttokens NA attr 23.2.0 attrs 23.2.0 babel 2.14.0 bleach 6.1.0 brotli 1.1.0 bs4 4.12.3 cerberus 1.3.5 certifi 2024.02.02 cffi 1.16.0 charset_normalizer 3.3.2 colorama 0.4.6 comm 0.2.2 cycler 0.12.1 cython_runtime NA dateutil 2.9.0 debugpy 1.8.1 decorator 5.1.1 defusedxml 0.7.1 dill 0.3.8 executing 2.0.1 fastjsonschema NA fqdn NA h5py 3.11.0 idna 3.7 igraph 0.11.5 ipykernel 6.29.3 isoduration NA jedi 0.19.1 jinja2 3.1.4 joblib 1.4.2 json5 0.9.25 jsonpointer 2.4 jsonschema 4.22.0 jsonschema_specifications NA jupyter_events 0.10.0 jupyter_server 2.14.1 jupyterlab_pygments 0.3.0 jupyterlab_server 2.27.2 kiwisolver 1.4.5 lazy_loader 0.4 legacy_api_wrap NA leidenalg 0.10.2 llvmlite 0.42.0 markupsafe 2.1.5 matplotlib_inline 0.1.7 mistune 3.0.2 mizani 0.11.4 mpl_toolkits NA natsort 8.4.0 nbclient 0.10.0 nbconvert 7.16.4 nbformat 5.10.4 numba 0.59.1 overrides NA packaging 24.0 pandocfilters NA parso 0.8.4 patsy 0.5.6 pickleshare 0.7.5 pkg_resources NA platformdirs 4.2.2 plotnine 0.13.6 pretty_jupyter NA prometheus_client NA prompt_toolkit 3.0.42 psutil 5.9.8 pure_eval 0.2.2 pycparser 2.22 pydev_ipython NA pydevconsole NA pydevd 2.9.5 pydevd_file_utils NA pydevd_plugins NA pydevd_tracing NA pygments 2.18.0 pynndescent 0.5.12 pyparsing 3.1.2 pythonjsonlogger NA pytz 2024.1 referencing NA rfc3339_validator 0.1.4 rfc3986_validator 0.1.1 rpds NA send2trash NA setuptools 70.0.0 six 1.16.0 skimage 0.22.0 sklearn 1.5.0 sniffio 1.3.1 socks 1.7.1 soupsieve 2.5 stack_data 0.6.2 statsmodels 0.14.2 texttable 1.7.0 threadpoolctl 3.5.0 tinycss2 1.3.0 tornado 6.4 tqdm 4.66.4 traitlets 5.14.3 typing_extensions NA umap 0.5.5 uri_template NA urllib3 2.2.1 wcwidth 0.2.13 webcolors 1.13 webencodings 0.5.1 websocket 1.8.0 yaml 6.0.1 zmq 26.0.3
----- IPython 8.25.0 jupyter_client 8.6.2 jupyter_core 5.7.2 jupyterlab 4.2.1 ----- Python 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0] Linux-6.8.0-35-generic-x86_64-with-glibc2.39 ----- Session information updated at 2024-06-07 11:33